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Weird Problem with New Messages.

I am having a problem with Zimbra since we went with the Network Version 6.0.
I did not notice this problem in the Open Source Version 5 edition we were using.

I am getting users reporting and have experienced myself an issue that new e-mail doesn't always show up in the Inbox when the web client is left running.
The number of new e-mails next to the Inbox reports accurately and if you click the Inbox folder again most of the time the missing messages will show up.

Was wondering if anyone has seen this problem or had any recommendations on what to try to do to fix this?